York: I hope Harbaugh has “all the leverage”

San Francisco owner Jed York said Thursday that he plans to sit down with coach Jim Harbaugh in the offseason to make the coach a formal offer on a contract extension. York said he’s hoping that extension makes Harbaugh one of the highest paid coaches in the NFL.

“I hope he has all the leverage in the world,” York said. “We kind of started to talk about a new contract last offseason after the Super Bowl, but it never got to the formal stage of making an offer. I think, rightfully so, Jim believes he has outperformed the original contract.”

In 2011, Harbaugh signed a five-year, $25 million contract after the 49ers hired him away from Stanford University. By the end of last season, Harbaugh was the lowest-paid coach in the NFC West on an average basis, trailing Seattle’s Pete Carroll ($7 million annually), Jeff Fisher of St. Louis ($6.5 million) and then-Arizona coach Ken Whisenhunt ($5.5 million).

“We’ll talk about something in the offseason that will put him in better position and we’ll see what he wants to do,” York said. “He does have two years left and he may decide to play it out and bet on himself. By the time the deal is done, maybe he’ll be worth $8 or $9 million a year because he has won a couple of Super Bowls. I sure hope that’s the case.”

On Thursday, Harbaugh said he “absolutely” wants to stay with the 49ers. Three sources close to Harbaugh said he has no interest at all in going to a college team, such as the University of Texas. Harbaugh has little or no patience for the glad-handing and politics that go with college programs.

York reiterated the point he made Wednesday on two San Francisco radio stations that there is some natural tension in the 49ers offices between Harbaugh and General Manager Trent Baalke. But York said the men have consistently worked out their differences to find the best solution for the 49ers.

“You’re talking about two men who don’t just want to be good at what they do, they want to be the best ever at what they do. When you have that, you have very opinionated people who don’t always agree on everything,” York said. “But they work it out.”

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